Single-cell omics: experimental workflow, data analyses and applications

F Sun, H Li, D Sun, S Fu, L Gu, X Shao, Q Wang… - Science China Life …, 2025 - Springer
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

S Ma, Y Zhang - Molecular biomedicine, 2020 - Springer
Chromatin regulatory landscape plays a critical role in many disease processes and embryo
development. Epigenome sequencing technologies such as chromatin immunoprecipitation …

Development of double-positive thymocytes at single-cell resolution

Y Li, K Li, L Zhu, B Li, D Zong, P Cai, C Jiang, P Du… - Genome Medicine, 2021 - Springer
Background T cells generated from thymopoiesis are essential for the immune system, and
recent single-cell studies have contributed to our understanding of the development of …

Machine learning for deciphering cell heterogeneity and gene regulation

M Scherer, F Schmidt, O Lazareva, J Walter… - Nature Computational …, 2021 - nature.com
Epigenetics studies inheritable and reversible modifications of DNA that allow cells to
control gene expression throughout their development and in response to environmental …

Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution

Q Yu, X Liu, J Fang, H Wu, C Guo, W Zhang, N Liu… - Science …, 2023 - science.org
Although mitotic chromosomes are highly compacted and transcriptionally inert, some active
chromatin features are retained during mitosis to ensure the proper postmitotic …

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA

SS Hu, L Liu, Q Li, W Ma, MJ Guertin, CA Meyer… - Nature …, 2022 - nature.com
Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been
widely used to identify regulatory DNA elements and transcription factor binding sites …

Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?

Y Liu, J Zhang, S Wang, X Zeng… - Briefings in …, 2022 - academic.oup.com
The tremendous progress of single-cell sequencing technology has given researchers the
opportunity to study cell development and differentiation processes at single-cell resolution …

simATAC: a single-cell ATAC-seq simulation framework

Z Navidi, L Zhang, B Wang - Genome biology, 2021 - Springer
Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies
regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is …

TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes

GW Schwartz, Y Zhou, J Petrovic, WS Pear, RB Faryabi - Cell reports, 2021 - cell.com
Emerging single-cell epigenomic assays are used to investigate the heterogeneity of
chromatin activity and its function. However, identifying cells with distinct regulatory …

Fundamental and practical approaches for single-cell ATAC-seq analysis

P Shi, Y Nie, J Yang, W Zhang, Z Tang, J Xu - Abiotech, 2022 - Springer
Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-
seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With …